Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues
European sardine or pilchard is a planktonic small pelagic fish present from the North Sea in Europe to the coast of Senegal in the North of Africa, and across the Mediterranean sea to the Black Sea. Ecologically, sardines are an intermediary link in the trophic network, preying on plankton and bein...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2021-12-01
|
| Series: | Data in Brief |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352340921008581 |
| _version_ | 1819174934611492864 |
|---|---|
| author | Jorge Langa Martin Huret Iratxe Montes Darrell Conklin Andone Estonba |
| author_facet | Jorge Langa Martin Huret Iratxe Montes Darrell Conklin Andone Estonba |
| author_sort | Jorge Langa |
| collection | DOAJ |
| description | European sardine or pilchard is a planktonic small pelagic fish present from the North Sea in Europe to the coast of Senegal in the North of Africa, and across the Mediterranean sea to the Black Sea. Ecologically, sardines are an intermediary link in the trophic network, preying on plankton and being predated by larger fishes, marine mammals, and seabirds. This species is of great nutritional and economic value as a cheap but rich source of protein and fat. It is either consumed directly by humans or fed as fishmeal for aquaculture and farm animals. Despite its importance in the food basket, little is known about the molecular mechanisms involved in protein and lipid synthesis in this species. We collected nine tissues of Sardina pilchardus and reconstructed the transcriptome. In all, 198,597 transcripts were obtained, from which 68,031 are protein-coding. Quality assessment of the transcriptome was performed by back-mapping reads to the transcriptome and by searching for Single Copy Orthologs. Additionally, Gene Ontology and KEGG annotations were retrieved for most of the protein-coding genes. Finally, each library was quantified in terms of Transcripts per Million to disclose their expression patterns. |
| first_indexed | 2024-12-22T20:46:52Z |
| format | Article |
| id | doaj.art-0a3605dcd76a4a308cb36e50e7214a85 |
| institution | Directory Open Access Journal |
| issn | 2352-3409 |
| language | English |
| last_indexed | 2024-12-22T20:46:52Z |
| publishDate | 2021-12-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Data in Brief |
| spelling | doaj.art-0a3605dcd76a4a308cb36e50e7214a852022-12-21T18:13:12ZengElsevierData in Brief2352-34092021-12-0139107583Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissuesJorge Langa0Martin Huret1Iratxe Montes2Darrell Conklin3Andone Estonba4Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Bizkaia 48940, SpainIFREMER, STH/LBH, B.P. 70, Plouzané 29280 FranceDepartment of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Bizkaia 48940, SpainDepartment of Computer Science and Artificial Intelligence, Faculty of Computer Science, University of the Basque Country UPV/EHU, San Sebastián, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, SpainDepartment of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Bizkaia 48940, Spain; Corresponding author.European sardine or pilchard is a planktonic small pelagic fish present from the North Sea in Europe to the coast of Senegal in the North of Africa, and across the Mediterranean sea to the Black Sea. Ecologically, sardines are an intermediary link in the trophic network, preying on plankton and being predated by larger fishes, marine mammals, and seabirds. This species is of great nutritional and economic value as a cheap but rich source of protein and fat. It is either consumed directly by humans or fed as fishmeal for aquaculture and farm animals. Despite its importance in the food basket, little is known about the molecular mechanisms involved in protein and lipid synthesis in this species. We collected nine tissues of Sardina pilchardus and reconstructed the transcriptome. In all, 198,597 transcripts were obtained, from which 68,031 are protein-coding. Quality assessment of the transcriptome was performed by back-mapping reads to the transcriptome and by searching for Single Copy Orthologs. Additionally, Gene Ontology and KEGG annotations were retrieved for most of the protein-coding genes. Finally, each library was quantified in terms of Transcripts per Million to disclose their expression patterns.http://www.sciencedirect.com/science/article/pii/S2352340921008581Sardina pilchardusEuropean sardineTranscriptome assemblyAnnotationExpressionTissue quantification |
| spellingShingle | Jorge Langa Martin Huret Iratxe Montes Darrell Conklin Andone Estonba Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues Data in Brief Sardina pilchardus European sardine Transcriptome assembly Annotation Expression Tissue quantification |
| title | Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues |
| title_full | Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues |
| title_fullStr | Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues |
| title_full_unstemmed | Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues |
| title_short | Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues |
| title_sort | transcriptomic dataset for sardina pilchardus assembly annotation and expression of nine tissues |
| topic | Sardina pilchardus European sardine Transcriptome assembly Annotation Expression Tissue quantification |
| url | http://www.sciencedirect.com/science/article/pii/S2352340921008581 |
| work_keys_str_mv | AT jorgelanga transcriptomicdatasetforsardinapilchardusassemblyannotationandexpressionofninetissues AT martinhuret transcriptomicdatasetforsardinapilchardusassemblyannotationandexpressionofninetissues AT iratxemontes transcriptomicdatasetforsardinapilchardusassemblyannotationandexpressionofninetissues AT darrellconklin transcriptomicdatasetforsardinapilchardusassemblyannotationandexpressionofninetissues AT andoneestonba transcriptomicdatasetforsardinapilchardusassemblyannotationandexpressionofninetissues |